POP5

protein-coding

POP5 homolog, ribonuclease P/MRP subunit

Gene summary

Enables ribonuclease P RNA binding activity. Contributes to ribonuclease P activity. Involved in tRNA 5'-leader removal. Located in nucleolus and nucleoplasm. Part of multimeric ribonuclease P complex and ribonuclease MRP complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_015918.4

Inheritance

—

ClinVar variants

U:17

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.96

Max pathogenic AF

—

Genomic locus

chr12:120,578,764-120,581,402

External References & Databases

Ensembl (ENSG00000167272)

Transcript & Mutation Effects

hg38 • Region Span ~2.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to POP5 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 16

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015918.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			16 clinvar			16
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	17	0	0	17

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 47 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015918.4	RefSeq	NP_057002.2	5	MANE Select
ENST00000357500.5	Ensembl	ENSP00000350098.4	5	MANE Select
NM_198202.2	RefSeq	NP_937845.1	4	Standard
ENST00000341039.6	Ensembl	ENSP00000341791.2	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ribosome biogenesis in eukaryotes - Homo sapiens (human)
RNA transport - Homo sapiens (human)
tRNA processing
Metabolism of RNA
tRNA processing in the nucleus

Biological Process

tRNA 5'-leader removal
rRNA processing
tRNA processing
RNA phosphodiester bond hydrolysis, endonucleolytic

Molecular Function

ribonuclease P activity
protein binding

Cellular Component

ribonuclease MRP complex
nucleoplasm
nucleolar ribonuclease P complex
multimeric ribonuclease P complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000357500
Coding exons: 5
Length: 2635
Individuals with no LoFs: 125721
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 125748
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.527	78	92.3	0.845	0.00000438	1043
Missense (PolyPhen)		34	36.504	0.93141		406
Synonymous	0.692	31	36.3	0.854	0.00000161	313
Loss of Function	0.122	10	10.4	0.959	5.79e-7	106

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00042	0.00042	rare
European (Non-Finnish)	0.00013	0.00013	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Also a component of RNase MRP. {ECO:0000269|PubMed:11413139}.;

Recessive Scores

pRec: 0.142

Intolerance Scores

LoFtool: 0.419
RVIS EVS: -0.16
RVIS percentile EVS: 41.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.786

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium